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Genetics Home Reference: your guide to understanding genetic conditions     A service of the U.S. National Library of Medicine®

Chromosome 3

Reviewed August 2015

What is chromosome 3?

Humans normally have 46 chromosomes in each cell, divided into 23 pairs. Two copies of chromosome 3, one copy inherited from each parent, form one of the pairs. Chromosome 3 spans about 198 million base pairs (the building blocks of DNA) and represents approximately 6.5 percent of the total DNA in cells.

Identifying genes on each chromosome is an active area of genetic research. Because researchers use different approaches to predict the number of genes on each chromosome, the estimated number of genes varies. Chromosome 3 likely contains 1,000 to 1,100 genes that provide instructions for making proteins. These proteins perform a variety of different roles in the body.

Genes on chromosome 3 are among the estimated 20,000 to 25,000 total genes in the human genome.

Genetics Home Reference provides information about the following genes on chromosome 3:

  • ABHD5
  • ACY1
  • ADCY5
  • AGTR1
  • AMT
  • ARHGAP31
  • ATP2C1
  • BCHE
  • BTD
  • CASR
  • CAV3
  • CHMP2B
  • CLRN1
  • CNBP
  • COL7A1
  • COLQ
  • CP
  • CPOX
  • CTNNB1
  • DNAJC19
  • EIF2B5
  • EOGT
  • FLNB
  • FOXL2
  • GBE1
  • GLB1
  • GNAT1
  • HESX1
  • HGD
  • HPS3
  • IFT80
  • IFT122
  • LARS2
  • LIPH
  • MASP1
  • MCCC1
  • MITF
  • MLH1
  • MYD88
  • NBEAL2
  • OPA1
  • PCCB
  • PDCD10
  • PDHB
  • PIK3CA
  • PROK2
  • PROS1
  • RAB7A
  • RAF1
  • RHO
  • RPL35A
  • SCN5A
  • SCN10A
  • SGOL1
  • SI
  • SLC25A20
  • SOX2
  • SUMF1
  • TERC
  • TGFBR2
  • THPO
  • TP63
  • TREX1
  • TSEN2
  • VHL
  • WNT5A
  • XPC

How are changes in chromosome 3 related to health conditions?

Many genetic conditions are related to changes in particular genes on chromosome 3. This list of disorders associated with genes on chromosome 3 provides links to additional information.

Genetics Home Reference provides information about the following conditions related to genes on chromosome 3:

  • 3MC syndrome
  • 3-methylcrotonyl-CoA carboxylase deficiency
  • aceruloplasminemia
  • Adams-Oliver syndrome
  • ADCY5-related dyskinesia
  • adult polyglucosan body disease
  • Aicardi-Goutieres syndrome
  • alkaptonuria
  • aminoacylase 1 deficiency
  • ankyloblepharon-ectodermal defects-cleft lip/palate syndrome
  • asphyxiating thoracic dystrophy
  • atelosteogenesis type 1
  • atelosteogenesis type 3
  • autosomal dominant congenital stationary night blindness
  • autosomal dominant hypocalcemia
  • autosomal recessive hypotrichosis
  • benign chronic pemphigus
  • biotinidase deficiency
  • blepharophimosis, ptosis, and epicanthus inversus syndrome
  • boomerang dysplasia
  • Brugada syndrome
  • carnitine-acylcarnitine translocase deficiency
  • CAV3-related distal myopathy
  • cerebral cavernous malformation
  • Chanarin-Dorfman syndrome
  • Charcot-Marie-Tooth disease
  • CHMP2B-related frontotemporal dementia
  • chronic atrial and intestinal dysrhythmia
  • combined pituitary hormone deficiency
  • congenital myasthenic syndrome
  • congenital sucrase-isomaltase deficiency
  • cranioectodermal dysplasia
  • desmoid tumor
  • Diamond-Blackfan anemia
  • dilated cardiomyopathy with ataxia syndrome
  • dyskeratosis congenita
  • dystrophic epidermolysis bullosa
  • essential thrombocythemia
  • familial dilated cardiomyopathy
  • familial encephalopathy with neuroserpin inclusion bodies
  • familial erythrocytosis
  • familial isolated hyperparathyroidism
  • familial thoracic aortic aneurysm and dissection
  • glycine encephalopathy
  • glycogen storage disease type IV
  • GM1 gangliosidosis
  • gray platelet syndrome
  • head and neck squamous cell carcinoma
  • Hermansky-Pudlak syndrome
  • idiopathic pulmonary fibrosis
  • isolated hyperCKemia
  • Kallmann syndrome
  • Larsen syndrome
  • Leigh syndrome
  • leukoencephalopathy with vanishing white matter
  • limb-girdle muscular dystrophy
  • Loeys-Dietz syndrome
  • lung cancer
  • Lynch syndrome
  • megalencephaly-capillary malformation syndrome
  • microphthalmia
  • mucopolysaccharidosis type IV
  • multiple lentigines syndrome
  • multiple sulfatase deficiency
  • MyD88 deficiency
  • myotonic dystrophy
  • nonsyndromic paraganglioma
  • Noonan syndrome
  • optic atrophy type 1
  • osteogenesis imperfecta
  • ovarian cancer
  • Perrault syndrome
  • pilomatricoma
  • pontocerebellar hypoplasia
  • porphyria
  • progressive familial heart block
  • propionic acidemia
  • protein S deficiency
  • pseudocholinesterase deficiency
  • pyruvate dehydrogenase deficiency
  • renal tubular dysgenesis
  • retinitis pigmentosa
  • rippling muscle disease
  • Robinow syndrome
  • Romano-Ward syndrome
  • septo-optic dysplasia
  • sick sinus syndrome
  • small fiber neuropathy
  • SOX2 anophthalmia syndrome
  • spondylocarpotarsal synostosis syndrome
  • systemic lupus erythematosus
  • Tietz syndrome
  • Usher syndrome
  • von Hippel-Lindau syndrome
  • Waardenburg syndrome
  • Waldenström macroglobulinemia
  • xeroderma pigmentosum

Is there a standard way to diagram chromosome 3?

Geneticists use diagrams called ideograms as a standard representation for chromosomes. Ideograms show a chromosome's relative size and its banding pattern. A banding pattern is the characteristic pattern of dark and light bands that appears when a chromosome is stained with a chemical solution and then viewed under a microscope. These bands are used to describe the location of genes on each chromosome.

Ideogram of chromosome 3
See How do geneticists indicate the location of a gene? ( in the Handbook.

Where can I find additional information about chromosome 3?

You may find the following resources about chromosome 3 helpful. These materials are written for the general public.

You may also be interested in these resources, which are designed for genetics professionals and researchers.

What glossary definitions help with understanding chromosome 3?

cell ; chromosome ; DNA ; inherited

You may find definitions for these and many other terms in the Genetics Home Reference Glossary.


  • Ensembl Human Map View: Chromosome 3 (;r=3:1-198022430)
  • Map Viewer: Genes on Sequence (,ugHs,genes&CHR=3)
  • Muzny DM, Scherer SE, Kaul R, Wang J, Yu J, Sudbrak R, Buhay CJ, Chen R, Cree A, Ding Y, Dugan-Rocha S, Gill R, Gunaratne P, Harris RA, Hawes AC, Hernandez J, Hodgson AV, Hume J, Jackson A, Khan ZM, Kovar-Smith C, Lewis LR, Lozado RJ, Metzker ML, Milosavljevic A, Miner GR, Morgan MB, Nazareth LV, Scott G, Sodergren E, Song XZ, Steffen D, Wei S, Wheeler DA, Wright MW, Worley KC, Yuan Y, Zhang Z, Adams CQ, Ansari-Lari MA, Ayele M, Brown MJ, Chen G, Chen Z, Clendenning J, Clerc-Blankenburg KP, Chen R, Chen Z, Davis C, Delgado O, Dinh HH, Dong W, Draper H, Ernst S, Fu G, Gonzalez-Garay ML, Garcia DK, Gillett W, Gu J, Hao B, Haugen E, Havlak P, He X, Hennig S, Hu S, Huang W, Jackson LR, Jacob LS, Kelly SH, Kube M, Levy R, Li Z, Liu B, Liu J, Liu W, Lu J, Maheshwari M, Nguyen BV, Okwuonu GO, Palmeiri A, Pasternak S, Perez LM, Phelps KA, Plopper FJ, Qiang B, Raymond C, Rodriguez R, Saenphimmachak C, Santibanez J, Shen H, Shen Y, Subramanian S, Tabor PE, Verduzco D, Waldron L, Wang J, Wang J, Wang Q, Williams GA, Wong GK, Yao Z, Zhang J, Zhang X, Zhao G, Zhou J, Zhou Y, Nelson D, Lehrach H, Reinhardt R, Naylor SL, Yang H, Olson M, Weinstock G, Gibbs RA. The DNA sequence, annotation and analysis of human chromosome 3. Nature. 2006 Apr 27;440(7088):1194-8. (
  • UCSC Genome Browser: Statistics (


The resources on this site should not be used as a substitute for professional medical care or advice. Users seeking information about a personal genetic disease, syndrome, or condition should consult with a qualified healthcare professional. See How can I find a genetics professional in my area? ( in the Handbook.

Reviewed: August 2015
Published: February 1, 2016